Fireflow: a library to read and write standards-compliant FCS files

FCS (flow cytometry standard) files are the canonical format for storing data produced by flow cytometers.

Supported FCS versions:

• 2.0
• 3.0
• 3.1
• 3.2

Key features:

• Is written in Rust (reliable and fast)
• Implements/enforces the FCS standard (see implementation details)
• Can convert between FCS versions
• Can repair non-compliant FCS files (see common issues)
• Has API for command line, Python, R (planned)

Status

Pre-release

API support

In addition to the core Rust library, fireflow has several wrappers.

Python

The Python wrapper for fireflow is pyreflow.

pyreflow is not yet available via PyPI or other package respositories so it must be built from source:

Install using pip/git:

pip install git+https://github.com/usnistgov/fireflow.git#subdirectory=pyreflow

This will build and install the master branch into the currently active environment.

Alternatively, install into a conda environment.

Example env.yml:

channels:
  - conda-forge
dependencies:
  - maturin=1.8.7
  - pip:
    - git+https://github.com/usnistgov/fireflow.git#subdirectory=pyreflow

The documentation is currently not hosted, so it needs to be built locally.

Run the following (assuming you have make installed):

make docs

Then open the resulting index file in a web browser: pyreflow/docs/build/html/index.html

Command Line Interface

See here.

R

Coming soon

Development and Support

This library was developed as part of the ongoing efforts of the NIST Flow Cytometry Standards Consortium.

Please submit code-related issues to the issue tracker in this repository. Please send general inquiries to [email protected].